Gene loci information

Transcript annotation

  • This transcript has been annotated as UDP-glucose 4-epimerase.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g8111 g8111.t1 TTS g8111.t1 28625930 28625930
chr_2 g8111 g8111.t1 isoform g8111.t1 28626116 28628114
chr_2 g8111 g8111.t1 exon g8111.t1.exon1 28626116 28626649
chr_2 g8111 g8111.t1 cds g8111.t1.CDS1 28626116 28626649
chr_2 g8111 g8111.t1 exon g8111.t1.exon2 28626707 28626997
chr_2 g8111 g8111.t1 cds g8111.t1.CDS2 28626707 28626997
chr_2 g8111 g8111.t1 exon g8111.t1.exon3 28627875 28628114
chr_2 g8111 g8111.t1 cds g8111.t1.CDS3 28627875 28628114
chr_2 g8111 g8111.t1 TSS g8111.t1 28628234 28628234

Sequences

>g8111.t1 Gene=g8111 Length=1065
ATGCTGTCAACAATATTAACAACAGGAGGTGCAGGATTCATTGGAAGCCACACAGTTTTA
GAGCTTCTTAATGCTGGTCATAATGTAATTTGCATTGATAATGAATGCAATGCTTATCAT
GAAAAAAATGAATTGCTGCCAGAATCATTAAAAAGAGTAGAAGAAATAACTGGAAAGAAT
GTCACTTATTATAATGTGGATATACGAGATAAAAACGCTCTAAGTTCGGTTTTTAAAAAG
CACAAAATCGATTGTGTTATTCATTTTGCTGCACTCAAGGCCGTAGGAGAATCATGTCGA
TTACCGCTACAATATTATCAAAATAACATAACTGGCACTTCCGTTTTACTTGAAGTAATG
ACTGAAAATCAAGTTTTTAATTTTGTGTATAGCAGCAGTGCAACAGTTTATGGAGACCCA
ATTTTCTTGCCTATAACAGAAGAACATCCTACCGGTGCATGTACAAATCCTTATGGTAAA
AGTAAATATTTTACCGAAGAAATATTGAAAGATTTATGTGTTTCTGATAATCGCTGGAAT
GTTATCTCATTGAGATATTTTAATCCTGTTGGAGCTCATAAATCAGGAAAAATCGGAGAA
GATCCAAATGGAGAACCTAATAACTTAATGCCATATATTTCGCAAGTTGCTGTTGGAAAA
CGAACATTGTTAAGAATTTTTGGTAATGATTATGCTACCGAAGACGGCACAGGAGTAAGG
GATTACATTCATATTGTTGATCTTGCTCAAGGACATCTATCCGCTCTAAATAAGTTGATT
GAAGGTGGATTGAGAGGATTTGCTGTTTATAATTTGGGAACTGGCAAGGGTTATTCAGTT
TTAGACATGGTAAAAAATTTTTCTACTGCATGCGGAATAGACATTCCATATGAATTCACG
TCTCGTCGAGATGGAGATATTGCCGCATGTTATGCTAGTACTGAAAAAGCTGAAAAAGAA
CTTGGTTGGAAGGCAAAATATGGAATCAAAGAAATGTGTGAAGACACATGGAGATGGCAG
AAAAATAATCCTAATGGATTTGCTGCATTAAAATCCGATCTCTAG

>g8111.t1 Gene=g8111 Length=354
MLSTILTTGGAGFIGSHTVLELLNAGHNVICIDNECNAYHEKNELLPESLKRVEEITGKN
VTYYNVDIRDKNALSSVFKKHKIDCVIHFAALKAVGESCRLPLQYYQNNITGTSVLLEVM
TENQVFNFVYSSSATVYGDPIFLPITEEHPTGACTNPYGKSKYFTEEILKDLCVSDNRWN
VISLRYFNPVGAHKSGKIGEDPNGEPNNLMPYISQVAVGKRTLLRIFGNDYATEDGTGVR
DYIHIVDLAQGHLSALNKLIEGGLRGFAVYNLGTGKGYSVLDMVKNFSTACGIDIPYEFT
SRRDGDIAACYASTEKAEKELGWKAKYGIKEMCEDTWRWQKNNPNGFAALKSDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g8111.t1 CDD cd05247 UDP_G4E_1_SDR_e 4 341 0e+00
8 g8111.t1 Gene3D G3DSA:3.40.50.720 - 5 285 0e+00
9 g8111.t1 Gene3D G3DSA:3.90.25.10 - 203 340 0e+00
2 g8111.t1 PANTHER PTHR43725:SF14 UDP-GLUCOSE 4-EPIMERASE 3 348 0e+00
3 g8111.t1 PANTHER PTHR43725 UDP-GLUCOSE 4-EPIMERASE 3 348 0e+00
4 g8111.t1 PRINTS PR01713 Nucleotide sugar epimerase signature 240 255 9e-07
6 g8111.t1 PRINTS PR01713 Nucleotide sugar epimerase signature 267 282 9e-07
5 g8111.t1 PRINTS PR01713 Nucleotide sugar epimerase signature 306 323 9e-07
1 g8111.t1 Pfam PF16363 GDP-mannose 4,6 dehydratase 6 336 0e+00
7 g8111.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 3 346 0e+00
10 g8111.t1 TIGRFAM TIGR01179 galE: UDP-glucose 4-epimerase GalE 5 346 0e+00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006012 galactose metabolic process BP
GO:0003978 UDP-glucose 4-epimerase activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values